Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttttttcctatgttgatgaagtaattcttgcttatttagttcagtgatcagtttatgaatcttttgtgtactataccatcaattgtgagatgagcacgatctgatttactaaattcacagATTGCATTGGGTAACATATTGAAGTTCCGCAAAAAGAATTGGCAGTTTGACATCATTGGCGGTTTTATATACTTCATTTTGGTGTTTTCAATGTTCCCAC

Basic information

species Zea mays
transcript GRMZM2G135839_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135839_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os07g01540.1 (Oryza sativa), 3'ss of exon 11
gtatgttttttcctatgttgatgaagtaattcttgcttatttagttcagtgatcagtttatgaatcttttgtgtactataccatcaattgtgagatgagcacgatctgatttactaaattcacagATTGCATTGGGTAACATATTGAAGTTCCGCAAAAAGAATTGGCAGTTTGACATCATTGGCGGTTTTATATACTTCATTTTGGTGTTTTCAATGTTCCCAC
||||||| ||  ||||| | ||| | |  ||||    | | |||   |   |  || ||| | | ||| | |||  | ||| |      |||| || || |  |||| ||  | |||||   ||||||||  ||||||| ||| | ||||||||||| |||||||||||||||||||  ||||| |||||||| ||||||||  |||| || |||||||||||||
gtatgttgttctctatgataatggaat--ttctgaaatttatagccta---actagcttaagtagcttgtatgttgtgtacaa------gtgaaataagga-aatcttatcaattaaatatgcagATTGCGCTGGGTAATATACTAAAGTTCCGCAAGAAGAATTGGCAGTTTGACACAATTGGTGGTTTTATCTACTTCATACTGGTATTCTCAATGTTCCCAC

upper sequence: GRMZM2G135839_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv18s0001g11060.t01 (Vitis vinifera), 3'ss of exon 11
gtatgttttttcctatgttgatgaagtaattcttgcttatttagttcagtgatcagtttatgaatcttttgtgtactataccatcaattgtgagatgagcacgatctgat--ttactaaattcacagATTGCATTGGGTAACATATTGAAGTTCCGCAAAAAGAATTGGCAGTTTGACATCATTGGCGGTTTTATATACTTCATTTTGGTGTTTTCAATGTTCCCAC
    ||   |    |  |   |  |||     | |||| |  |   ||   ||    || |  ||   || | |  | | |  | ||||     || |  | | | |  |  | | |  ||   |||||||||||||| || || ||||||||||| || |||||||||||||||||  ||||||| ||  ||||||| ||  | ||||| ||||| ||||| ||||
----gtaaatctgaaaatc--tacagttccattggcttgtcaataccaaaaatttcattttatattcctttttt--tttccttttaatttctcaataa-tatggtgtattggtcatttgat--gcagATTGCATTGGGAAATATTTTGAAGTTCCGAAAGAAGAATTGGCAGTTTGATTTCATTGGTGGCATTATATATTTTGTATTGGTTTTTTCTATGTTTCCAC

upper sequence: GRMZM2G135839_T01 (Zea mays), 3'ss of exon 11
lower sequence: PP1S72_100V6.1 (Physcomitrella patens), 3'ss of exon 9
gtatgttttttcctatgttgatgaagtaattctt--gcttatttagttcagtgatcagtttatgaatcttttgtgtactataccatcaattgtgagatgagcacgatctgatttactaaattcacagATTGCATTGGGTAACATATTGAAGTTCCGCAAAAAGAATTGGCAGTTTGACATCATTGGCGGTTTTATATACTTCATTTTGGTGTTTTCAATGTTCCCAC
             |||||  || |    ||||||    ||| | |  |   ||  | || || ||     |  || || |  |     | |   | ||  |   | | || || ||     | ||||||||||| ||| ||||| |||||||| || || ||||||||||  |||||  | ||||| ||| || ||||||| || ||||| || |||||||||||||
------------gtatgtaaatcataacattcttcaaattactcaaatttatg-cctgtctaggacatgatattggacaaagcttatgagt---aaatttgtgtg-tatggtt-accttccttacagATTGCATGGGGAAACATCTTGAAGTTTCGAAAGAAGAATTGGCGTTTTGATGTAATTGGTGGTGTTGTATACTTTATATTGGTTTTCTCAATGTTCCCAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 16

CTTTTTGCACCCAACACATGTTTTCAGAAACTTTGAGAGGTTCTCTGGAACCACCTATGAATGCAAGGCAGCTTATCCATCCTATGATGAGTCTACTGGGgtatgttttt ... aaattcacagATTGCATTGGGTAACATATTGAAGTTCCGCAAAAAGAATTGGCAGTTTGACATCATTGGCGGTTTTATATACTTCATTTTGGTGTTTTCAATGTTCCCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 9

CTTTTTGCACCCAACACATGTTTTCAGAAACTTTGAGAGGTTCTCTGGAACCACCTATGAATGCAAGGCAGCTTATCCATCCTATGATGAGTCTACTGGGgtatgttttt ... aaattcacagATTGCATTGGGTAACATATTGAAGTTCCGCAAAAAGAATTGGCAGTTTGACATCATTGGCGGTTTTATATACTTCATTTTGGTGTTTTCAATGTTCCCAC


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 7

CTTTTTGCACCCAACACATGTTTTCAGAAACTTTGAGAGGTTCTCTGGAACCACCTATGAATGCAAGGCAGCTTATCCATCCTATGATGAGTCTACTGGGgtatgttttt ... aaattcacagATTGCATTGGGTAACATATTGAAGTTCCGCAAAAAGAATTGGCAGTTTGACATCATTGGCGGTTTTATATACTTCATTTTGGTGTTTTCAATGTTCCCAC


Block sizes: 48 (upstream exon), 41 (downstream exon)
Score: 15

CTTTTTGCACCCAACACATGTTTTCAGAAACTTTGAGAGGTTCTCTGGAACCACCTATGAATGCAAGGCAGCTTATCCATCCTATGATGAGTCTACTGGGgtatgttttt ... aaattcacagATTGCATTGGGTAACATATTGAAGTTCCGCAAAAAGAATTGGCAGTTTGACATCATTGGCGGTTTTATATACTTCATTTTGGTGTTTTCAATGTTCCCAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtactataccatcaattgtgagatgagcacgatctgatttactaaattcacagATTGCATTGGGTAACATATTGAAGTTCCGCAAAAAGAATTGGCAGTTTGACATCATTGGCGGTTTTATATACTTCATTTTGGTGTTTTCAATGTTCCCAC
                                         tactaaa  putative branch site (score: 15)
                                    tgatttactaaatt  TA-rich tract